Contacts of the strand formed by residues 191 - 197 (chain G) in PDB entry 3KYM
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 191 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149G LYS 4.0 0.7 - - - +
150G VAL* 3.8 3.5 - - - +
151G ASP* 2.9 54.6 + - - +
152G ASN* 4.9 6.0 + - - +
189G HIS 3.8 1.0 - - - -
190G LYS* 1.3 83.9 - - + +
192G TYR* 1.3 71.3 + - - +
193G ALA* 5.4 2.5 - - + -
208G SER* 4.5 10.5 - - - -
209G PHE 3.5 11.0 - - - +
210G ASN* 3.4 20.0 - - - +
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Residues in contact with TYR 192 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G ILE* 4.5 2.6 - - + +
132G VAL* 4.6 8.5 - - + -
148G TRP* 5.2 2.2 - - + -
149G LYS 3.6 2.9 - - - +
150G VAL* 3.7 30.3 - - + -
179G LEU* 4.5 11.4 - - + -
181G LEU* 4.3 14.5 - - + +
185G ASP 4.0 0.3 + - - -
186G TYR* 2.6 59.2 + + - -
189G HIS* 3.6 33.9 - - + +
190G LYS 4.6 1.1 - - - -
191G VAL* 1.3 79.2 - - - +
193G ALA* 1.3 63.2 + - - +
208G SER* 3.1 5.7 - - - -
209G PHE* 3.0 67.2 + + + -
211G ARG* 4.1 6.3 - - + -
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Residues in contact with ALA 193 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G ILE* 4.5 2.0 - - - -
147G GLN 3.7 0.7 - - - +
148G TRP* 3.6 10.2 - - - -
149G LYS* 2.8 50.1 + - + +
191G VAL* 5.4 2.5 - - + -
192G TYR* 1.3 78.1 - - - +
194G CYS* 1.3 60.6 + - - +
195G GLU 4.0 0.5 + - - -
206G THR* 4.2 12.3 - - + -
207G LYS 3.1 12.6 - - - +
208G SER* 3.5 12.8 - - - +
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Residues in contact with CYS 194 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G ILE* 4.3 5.7 - - + +
134G CYS* 2.0 51.1 - - + -
146G VAL* 3.4 25.4 - - - -
147G GLN 3.3 4.0 - - - -
148G TRP* 4.2 13.5 - - + -
193G ALA* 1.3 70.5 - - - +
195G GLU* 1.3 58.7 + - - +
196G VAL* 4.2 8.9 + - + +
205G VAL 3.8 0.7 - - - +
206G THR* 3.2 4.9 - - - -
207G LYS* 2.8 40.3 + - + +
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Residues in contact with GLU 195 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145G LYS 3.8 0.5 - - - +
146G VAL* 3.2 4.5 - - - -
147G GLN* 2.6 54.2 + - + +
149G LYS* 2.8 38.6 + - + +
193G ALA 4.0 1.4 + - - -
194G CYS* 1.3 69.4 - - - +
196G VAL* 1.3 65.9 + - - +
197G THR* 5.2 2.9 + - - +
204G PRO* 3.9 25.6 - - + +
205G VAL 3.3 5.4 - - - +
206G THR* 3.3 17.0 + - + +
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Residues in contact with VAL 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G PRO* 4.6 7.6 - - + -
115G VAL* 3.7 37.5 - - + -
136G LEU* 3.9 31.2 - - + -
144G ALA* 5.4 0.4 - - + -
145G LYS 3.3 6.3 - - - +
146G VAL* 4.6 3.6 - - + -
194G CYS* 4.3 12.1 - - - +
195G GLU* 1.3 79.6 - - - +
197G THR* 1.3 73.0 + - - +
198G HIS* 4.9 0.9 - - + -
201G LEU* 3.9 12.3 - - + +
204G PRO* 3.2 6.4 - - - +
205G VAL 2.7 41.3 + - - +
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Residues in contact with THR 197 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G ALA* 3.6 8.1 - - - +
145G LYS* 2.8 59.9 + - - +
195G GLU* 5.3 3.6 - - - +
196G VAL* 1.3 76.2 - - - +
198G HIS* 1.3 67.9 + - - +
204G PRO* 4.3 25.3 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il